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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaacccaaaaagtctctgtctttgtaagctgcaaagagaaagttttgctctctcttctgatttgagtctttggtgttcttagGCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATATGAGAATAAGGCACAGATGAATTCTATATCAATGCATCTTGGAGAGAGTG

Basic information

species Arabidopsis thaliana
transcript AT5G22950.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|163997449|gb|ES080156.1|ES080156
EST:     AGAAAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAG                         GCACTTGCTAAGGAAATTGTGAGTTC
genomic: AGAAAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAGgttagaaccc ... gtgttcttagGCACTTGCTAAGGAAATTGTGAGTTC
EST: gi|125253319|gb|EL267404.1|EL267404
EST:     AGAAAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAG                         GCACTTGCTAAGGAAATTGTGAG
genomic: AGAAAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAGgttagaaccc ... gtgttcttagGCACTTGCTAAGGAAATTGTGAG
EST: gi|125248614|gb|EL262699.1|EL262699
EST:     AAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAG                         GCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATA
genomic: AAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAGgttagaaccc ... gtgttcttagGCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATA
EST: gi|116474557|gb|EG517149.1|EG517149
EST:     AGAAAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAG                         GCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATAT
genomic: AGAAAGCTATTAAAGAAGCTGCAAAGAGGAATGATATGGTCTCTGCTAAGgttagaaccc ... gtgttcttagGCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgcaaagagaaagttttgctctctcttctgatttgagtctttggtgttcttagGCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATATGAGAATAAGGCACAGATGAATTCTATATCAATGCATCTTGGAGAGAGTG
                           ttctgat  putative branch site (score: 3)
                                              tgttctt  putative PPT
           aaagtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaacccaaaaagtctctgtctttgtaagctgcaaagagaaagttttgctctctcttctgatttgagtctttggtgttcttagGCACTTGCTAAGGAAATTGTGAGTTCGAGAAGAACAGTGAACCGGTTATATGAGAATAAGGCACAGATGAATTCTATATCAATGCATCTTGGAGAGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA